rs9904288

Variant names:

• chr17-48954611-T-C
• rs9904288

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.276 in 151,956 control chromosomes in the GnomAD database, including 6,089 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.28 (6089 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308
• Publications: 24 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.401 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.276 AC: 41888 AN: 151838 Hom.: 6087 Cov.: 31

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.365

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.290

Gnomad OTH AF: 0.276

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.276 AC: 41920 AN: 151956 Hom.: 6089 Cov.: 31 AF XY: 0.278 AC XY: 20624 AN XY: 74264

African (AFR) AF: 0.223 AC: 9257 AN: 41452

American (AMR) AF: 0.410 AC: 6232 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.365 AC: 1267 AN: 3470

East Asian (EAS) AF: 0.162 AC: 841 AN: 5180

South Asian (SAS) AF: 0.211 AC: 1017 AN: 4818

European-Finnish (FIN) AF: 0.251 AC: 2650 AN: 10558

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.290 AC: 19724 AN: 67954

Other (OTH) AF: 0.276 AC: 582 AN: 2108

Alfa AF: 0.285 Hom.: 6522

Bravo AF: 0.285

Asia WGS AF: 0.198 AC: 689 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.9
DANN	Benign	0.47
PhyloP100		0.31

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs9904288; hg19: chr17-47031973;